CDGo: A Wrapper for Analysing Circular Dichroism Spectroscopy Data

Installation

Easiest way to download is by using git:

git clone https://github.com/s-gordon/CDGo.git

Then install CDGo using your favourite python installation (v2.7+):

cd /path/to/cdgo/source
python setup.py install

There are several dependencies required by CDGo not found in many base python installations. These are listed in requirements_dev.txt and can be conveniently installed using the python package manager pip:

pip install -r requirements_dev.txt

Dependencies

• Wine
• Python 2.7+

Most of these can be installed through Homebrew (OSX) or your trusty Linux package manager.

OSX

brew install wine

Linux (Debian)

apt-get install wine

Linux (Fedora)

dnf install wine

Windows

No installation instructions are provided for Windows. This could potentially be extended using Cygwin, but would require configuring a complete Python environment as well as the dependencies called for by CDGo.

Alternatively, one could set up a unix-like environment on Windows by using a virtual machine (e.g. using VirtualBox).

Usage

cdgo [-h] [-C CDPRO_DIR] -i CDPRO_INPUT --mol_weight MOL_WEIGHT \
--number_residues NUMBER_RESIDUES --concentration CONCENTRATION \
[--buffer BUFFER] [--cdsstr] [--continll] [-v]

cdgo --help

Output will be written to a folder in the same directory as the input of the format <input>-CDPro.

Ongoing Issues

Input files with replicates

In the case where any input files from Aviv machines are passed to CDGo, it will throw an error along the lines of:

IndexError: index -1 is out of bounds for axis 0 with size 0

This is expected, and results from CDGo currently being unable to handle replicate data sets. This will change in the future, but for now you will need to either average the input data sets manually or simply remove all but one replicate from the input file.

Who do I talk to

• Shane Gordon
• Tao Nelson (original author)

Contributors

See contributors.txt

Citation

CDGo

CDGo is research software. If you make use of CDGo in scientific publications, please cite it. The BibTeX reference is as follows:

@misc{Gordon2016CDGo,
  author = {Gordon, S. E. and Nelson, T. G.},
  title = {CDGo: A Wrapper for Analysing Circular Dichroism Spectroscopy Data},
  year = {2016},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/s-gordon/cdgo}},
  }

CDPro

CDPro is research software. If you make use of CDGo in scientific publications, please cite it. The BibTeX reference is as follows:

@article{Sreerama2000CDPro,
  title = {Estimation of protein secondary structure from circular dichroism
           spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an
           expanded reference set},
  author = {Sreerama, Narasimha and Woody, Robert W},
  journal = {Analytical biochemistry},
  volume = {287},
  number = {2},
  pages = {252--260},
  year = {2000},
  publisher = {Elsevier}
}

Please refer to the CDPro webpage for further details.

CONTINLL

@article{Provencher:81,
   doi         = {10.1021/bi00504a006},
   url         = {https://doi.org/10.1021%2Fbi00504a006},
   year        = 1981,
   month       = {1},
   publisher   = {American Chemical Society ({ACS})},
   volume      = {20},
   number      = {1},
   pages       = {33--37},
   author      = {Stephen W. Provencher and Juergen Gloeckner},
   title       = {Estimation of globular protein secondary structure from
                  circular dichroism},
   journal     = {Biochemistry}
}

@article{van_Stokkum:90,
   doi         = {10.1016/0003-2697(90)90396-q},
   url         = {https://doi.org/10.1016%2F0003-2697%2890%2990396-q},
   year        = 1990,
   month       = {11},
   publisher   = {Elsevier {BV}},
   volume      = {191},
   number      = {1},
   pages       = {110--118},
   author      = {Ivo H.M. van Stokkum and Hans J.W. Spoelder and Michael
                  Bloemendal and Rienk van Grondelle and Frans C.A. Groen},
   title       = {Estimation of protein secondary structure and error analysis
                  from circular dichroism spectra},
   journal     = {Anal Biochem}
}

CDSSTR

@article{Sreerama:00,
   doi         = {10.1006/abio.2000.4880},
   url         = {https://doi.org/10.1006%2Fabio.2000.4880},
   year        = 2000,
   month       = {12},
   publisher   = {Elsevier {BV}},
   volume      = {287},
   number      = {2},
   pages       = {252--260},
   author      = {Narasimha Sreerama and Robert W. Woody},
   title       = {Estimation of Protein Secondary Structure from Circular
                  Dichroism Spectra: Comparison of {CONTIN}, {SELCON}, and
                  {CDSSTR} Methods with an Expanded Reference Set},
   journal     = {Anal Biochem}
}

@article{Johnson:99,
   title       = {Analyzing protein circular dichroism spectra for accurate
                  secondary structures},
   author      = {Johnson, W Curtis},
   journal     = {Proteins: Struct, Funct, Bioinf},
   volume      = {35},
   number      = {3},
   pages       = {307--312},
   year        = {1999},
   publisher   = {Wiley Online Library}
}

Everything Else

Generally refer to the website for CDPro.

Licence

See LICENSE.md